A koala pangenome reveals hidden structural variation with implications for disease and fertility

Structural variation is likely a major driver of adaptation yet has remained largely unexplored in wildlife genomics with most species represented by a single reference genome. This limitation is especially acute for wide-ranging species, where local adaptation, disease exposure and demographic history can vary dramatically. Here we construct the first marsupial pangenome from 13 long-read koala (Phascolarctos cinereus) genomes spanning the species’ range across eastern Australia. We identify approximately 193,000 SVs and half a gigabase of sequence absent from the current reference genome, revealing extensive unexplored diversity across populations. Within these variants we highlight candidate mechanisms underlying regional differences in disease susceptibility, retroviral biology, and fertility, including a duplication of a chlamydia-inhibiting cathelicidin, loss of trypsin-like genes implicated in viral entry, and a centromere-associated expansion of SUN2-like genes. Across the range, endogenous retroviruses are contributing to ongoing genome evolution. Our findings show that structural variation contributes substantially to functional genomic diversity in koalas and provide a framework for linking genome architecture to phenotypic divergence in threatened wildlife. More broadly, this work demonstrates how pangenomes can uncover adaptive variation that is difficult to detect using short-reads and single-reference approaches.